So the isolation valve was open while filling, but still got 1% difference. Did you open your isolation valve fully or just a little? Did you fill quickly from a storage tank or slowly from a compressor?
If the valve is just a quarter turn open, it will equalize during the dive and allow for a quick v-drill, but maybe it'll cause a pressure differential between the tanks during a fast fill?
Out of air with half-full tanks - Cave Diver Harry
I did not fill it myself. But, I often do fill my own tanks at that shop, so I'm pretty sure I know how they were filled. Isolator would have been all the way open. They would have been topped up with air using one fill whip, coming out of a manifold that has a restrictor in it that limits the fill rate to 500psi per minute (if I recall that spec correctly - which I might not be*). It would have been filled from a bank until (if) the highest bank pressure was not high enough, then been boosted to 3500 from there. The last fill I did myself, the high bank was a bit below 3500 and I did have to boost the last few hundred psi.
* Now that I typed that, I don't see how it's possible to have a restrictor that limits to a certain number of psi per minute. There's all kinds of things wrong with that concept. It does have some kind of flow limiter, but I'm going to have to ask about that next time I'm at the shop.